01-04-2016
Similar question, or related:
For "daily" jobs, perl/python/bash would be enough as my work is in bioinformatics.
I found out C/C++ maybe the "must-have" if any complicate problems like genome assembly (string searching & joining) with big data files are (10~100GB of millions of rows) normally used.
First skill is to handle big files;
Second is manipulation of data structures (suffix arrays, transformation of data format/structure) using smart algorithms.
Both need manage memory efficiently, and C/C++ seem the best choice, if not the only one as I know.
I was wondering what background are those softwares devloper? Guess they are majoring in software engineering. And how did they develop the prgoramming skilles? Or, how can I develop skills to glue the components together like the software enginner?
"Practice-practice-practice" is too vague to me. Especially I am stuck at the beginning.
Last edited by yifangt; 01-05-2016 at 03:38 PM..
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LEARN ABOUT DEBIAN
bp_process_gadfly
BP_PROCESS_GADFLY(1p) User Contributed Perl Documentation BP_PROCESS_GADFLY(1p)
NAME
process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
SYNOPSIS
% process_gadfly.pl ./RELEASE2 > gadfly.gff
DESCRIPTION
This script massages the RELEASE 3 Flybase/Gadfly GFF files located at http://www.fruitfly.org/sequence/release3download.shtml into the
"correct" version of the GFF format.
To use this script, download the whole genome FASTA file and save it to disk. (The downloaded file will be called something like
"na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the HTML page doesn't give the filename.) Do the same for the whole genome
GFF annotation file (the saved file will be called something like "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".) If you wish
you can download the ZIP compressed versions of these files.
Next run this script on the two files, indicating the name of the downloaded FASTA file first, followed by the gff file:
% process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database using the following command:
% bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff
(Where "fly" is the name of the database. Change it as appropriate. The database must already exist and be writable by you!)
The resulting database will have the following feature types (represented as "method:source"):
Component:arm A chromosome arm
Component:scaffold A chromosome scaffold (accession #)
Component:gap A gap in the assembly
clone:clonelocator A BAC clone
gene:gadfly A gene accession number
transcript:gadfly A transcript accession number
translation:gadfly A translation
codon:gadfly Significance unknown
exon:gadfly An exon
symbol:gadfly A classical gene symbol
similarity:blastn A BLASTN hit
similarity:blastx A BLASTX hit
similarity:sim4 EST->genome using SIM4
similarity:groupest EST->genome using GROUPEST
similarity:repeatmasker A repeat
IMPORTANT NOTE: This script will *only* work with the RELEASE3 gadfly files and will not work with earlier releases.
SEE ALSO
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
AUTHOR
Lincoln Stein, lstein@cshl.org
Copyright (c) 2002 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.2 2012-03-02 BP_PROCESS_GADFLY(1p)